Alexandra Zidovska

Cationic liposome-nucleic acid complexes for gene delivery and silencing: pathways and mechanisms for plasmid DNA and siRNA.

Motivated by the promises of gene therapy, there is great interest in developing non-viral lipid-based vectors for therapeutic applications due to their low immunogenicity, low toxicity, ease of production, and the potential of transferring large pieces of DNA into cells. In fact, cationic liposome (CL) based vectors are among the prevalent synthetic carriers of nucleic acids (NAs) currently used in gene therapy clinical trials worldwide. These vectors are studied both for gene delivery with CL-DNA complexes and gene silencing with CL-siRNA (short interfering RNA) complexes. However, their transfection efficiencies and silencing efficiencies remain low compared to those of engineered viral vectors. This reflects the currently poor understanding of transfection-related mechanisms at the molecular and self-assembled levels, including a lack of knowledge about interactions between membranes and double stranded NAs and between CL-NA complexes and cellular components. In this review we describe our recent efforts to improve the mechanistic understanding of transfection by CL-NA complexes, which will help to design optimal lipid-based carriers of DNA and siRNA for therapeutic gene delivery and gene silencing.

Micron-scale coherence in interphase chromatin dynamics

Significance Chromatin, the functional form of DNA inside the cell nucleus, has been heavily studied using biochemical and genetic methods, but we still know little about its large-scale organization and even less about its dynamics. We present a unique method, displacement correlation spectroscopy (DCS), which allows us to map interphase chromatin dynamics simultaneously across the entire nucleus and follow the temporal evolution of the global chromatin dynamics in vivo. Using DCS we discovered that chromatin moves coherently across micron-scale regions for a few seconds, which implies a transient mechanical coupling between chromatin on different chromosomes. This coupling might allow different regions of the nucleus to communicate by a unique, mechanochemical mechanism, e.g., to coordinate responses to DNA damage. Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood, especially at large length scales. We developed an approach, displacement correlation spectroscopy based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. This method revealed that chromatin movement was coherent across large regions (4–5 µm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes. These large-scale, coupled motions were ATP dependent and unidirectional for several seconds, perhaps accounting for ATP-dependent directed movement of single genes. Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II eliminated micron-scale coherence, while causing rapid, local movement to increase; i.e., local motions accelerated but became uncoupled from their neighbors. We observe similar trends in chromatin dynamics upon inducing a direct DNA damage; thus we hypothesize that this may be due to DNA damage responses that physically relax chromatin and block long-distance communication of forces.

The role of cholesterol and structurally related molecules in enhancing transfection of cationic liposome-DNA complexes.

Motivated by its important role in gene delivery, we have studied the effect of cholesterol and analogs on the transfection efficiency (TE) of lamellar cationic liposome-DNA (CL-DNA) complexes in vitro. Addition of cholesterol to low-transfecting DOTAP/DOPC-DNA complexes increases TE, with 15 mol % cholesterol already yielding 10-fold improvement. Steroids lacking the alkyl tail only modestly enhance TE, while molecules retaining it strongly enhance TE. All steroid-containing CL-DNA complexes exhibit the lamellar structure. The increase in experimentally determined membrane charge density (a universal parameter governing the TE of lamellar CL-DNA complexes) with cholesterol content alone cannot account for the rapid increase of TE. Instead, the reduction of the hydration repulsion layer of the membrane, caused by replacement of DOPC by cholesterol, promotes fusion between cationic membranes of CL-DNA complexes and anionic endosomal membranes, thus facilitating release of complexes and enhancing TE.

On the Mechanical Stabilization of Filopodia

We studied force-induced elongation of filopodia by coupling magnetic tweezers to the tip through the bacterial coat protein invasin, which couples the force generator to the actin bundles (through myosin X), thus impeding the growth of the actin plus end. Single force pulses (15-30 s) with amplitudes between 20 and 600 pN and staircase-like force scenarios (amplitudes, ∼50 pN; step widths, 30 s) were applied. In both cases, the responses consist of a fast viscoelastic deflection followed by a linear flow regime. The deflections are reversible after switching off the forces, suggesting a mechanical memory. The elongation velocity exhibits an exponential distribution (half-width , ∼0.02 μm s(-1)) and did not increase systematically with the force amplitudes. We estimate the bending modulus (0.4 × 10(-23) J m) and the number of actin filaments (∼10) by analyzing filopodium bending fluctuations. Sequestering of intracellular Ca(2+) by BAPTA caused a strong reduction in the amplitude of elongation, whereas latrunculin A resulted in loss of the elastic response. We attribute the force-independent velocity to the elongation of actin bundles enabled by the force-induced actin membrane uncoupling and the reversibility by the treadmilling mechanism and an elastic response.

Block Liposomes from Curvature-Stabilizing Lipids: Connected Nanotubes, -rods or -spheres

We report on the discovery of block liposomes, a new class of chain-melted (liquid) vesicles, with membranes comprised of mixtures of the membrane-curvature-stabilizing multivalent lipid MVLBG2 of colossal charge +16 e and neutral 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC). In a narrow MVLBG2 composition range (8-10 mol%), cryo-TEM revealed block liposomes consisting of distinctly shaped, yet connected, nanoscale spheres, pears, tubes, or rods. Unlike typical liposome systems, where spherical vesicles, tubular vesicles, and cylindrical micelles are separated on the macroscopic scale, within a block liposome, shapes are separated on the nanometer scale. Diblock (pear-tube) and triblock (pear-tube-pear) liposomes contain nanotubes with inner lumen diameter of 10-50 nm. Diblock (sphere-rod) liposomes were found to contain micellar nanorods approximately 4 nm in diameter and several micrometers in length, analogous to cytoskeletal filaments of eukaryotic cells. Block liposomes may find a range of applications in chemical and nucleic acid delivery and as building blocks in the design of templates for hierarchical structures.

Development of Time-Integrated Multipoint Moment Analysis for Spatially Resolved Fluctuation Spectroscopy with High Time Resolution

Spatial gradients in the behaviors of soluble proteins are thought to underlie many phenomena in cell and developmental biology, but the nature and even the existence of these gradients are often unclear because few techniques can adequately characterize them. Methods with sufficient temporal resolution to study the dynamics of diffusing molecules can only sample relatively small regions, whereas methods that are capable of imaging larger areas cannot probe fast timescales. To overcome these limitations, we developed and implemented time-integrated multipoint moment analysis (TIMMA), a form of fluorescence fluctuation spectroscopy that is capable of probing timescales down to 20 μs at hundreds of different locations simultaneously in a sample. We show that TIMMA can be used to measure the diffusion of small-molecule dyes and fluorescent colloids, and that it can create spatial maps of the behavior of soluble fluorescent proteins throughout mammalian tissue culture cells. We also demonstrate that TIMMA can characterize internal gradients in the diffusion of freely moving proteins in single cells.

Nanoscale Assembly in Biological Systems: From Neuronal Cytoskeletal Proteins to Curvature Stabilizing Lipids

The review will describe experiments inspired by the rich variety of bundles and networks of interacting microtubules (MT), neurofilaments, and filamentous-actin in neurons where the nature of the interactions, structures, and structure-function correlations remain poorly understood. We describe how three-dimensional (3D) MT bundles and 2D MT bundles may assemble, in cell free systems in the presence of counter-ions, revealing structures not predicted by polyelectrolyte theories. Interestingly, experiments reveal that the neuronal protein tau, an abundant MT-associated-protein in axons, modulates the MT diameter providing insight for the control of geometric parameters in bio- nanotechnology. In another set of experiments we describe lipid-protein-nanotubes, and lipid nano-tubes and rods, resulting from membrane shape evolution processes involving protein templates and curvature stabilizing lipids. Similar membrane shape changes, occurring in cells for the purpose of specific functions, are induced by interactions between membranes and proteins. The biological materials systems described have applications in bio-nanotechnology.

Block liposomes vesicles of charged lipids with distinctly shaped nanoscale sphere-, pear-, tube-, or rod-segments.

We describe the preparation and characterization of block liposomes, a new class of liquid (chain-melted) vesicles, from mixtures of the highly charged (+16 e) multivalent cationic lipid MVLBG2 and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC). Block liposomes (BLs) consist of distinct spherical, tubular vesicles, and cylindrical micelles that remain connected, forming a single liposome. This is in contrast to typical liposome systems, where distinctly shaped liposomes are macroscopically separated. In a narrow composition range (8-10 mol% MVLBG2), an abundance of micrometer-scale BLs (typically sphere-tube-sphere triblocks) is observed. Cryo-TEM reveals that BLs are also present at the nanometer scale, where the blocks consist of distinctly shaped nanoscale spheres, pears, tubes, or rods. Pear-tube diblock and pear-tube-pear triblock liposomes contain nanotubes with inner lumen diameter 10-50 nm. In addition, sphere-rod diblock liposomes are present, containing rigid micellar nanorods approximately 4 nm in diameter and several microm in length. Block liposomes may find a range of applications in chemical and nucleic acid delivery and as building blocks in the design of templates for hierarchical structures.

The Effect of Salt and pH on Block Liposomes studied by Cryogenic Transmission Electron Microscopy

Recently, we have reported the discovery of block liposomes (BLs), a new class of liquid (chain-melted) vesicles, formed in mixtures of the curvature-stabilizing hexadecavalent cationic lipid MVLBG2, the neutral lipid 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC), and water with no added salt. BLs consist of connected spheres, pears, tubes, or rods. Unlike in typical liposome systems, where spherical vesicles, tubular vesicles, and cylindrical micelles are separated on the macroscopic scale, shapes remain connected and are separated only on the nanometer scale within a single BL. Here, we report structural studies of the effect of salt and pH on the BL phase, carried out using differential interference contrast microscopy (DIC) and cryogenic transmission electron microscopy (cryo-TEM). Addition of salt screens the electrostatic interactions; in low-salt conditions, partial screening of electrostatic interactions leads to a shape transition from BLs to bilamellar vesicles, while in the high-salt regime, a shape transition from BLs to liposomes with spherical morphologies occurs. This demonstrates that strong electrostatic interactions are essential for BL formation. Understanding the control of liposome shape evolution is of high interest because such shape changes play an important role in many intracellular processes such as endocytosis, endoplasmatic reticulum-associated vesiculation, vesicle recycling and signaling.

Block liposome and nanotube formation is a general phenomenon of two-component membranes containing multivalent lipids

We report a study on the formation of block liposomes (BLs) and nanotubes from membranes comprised of mixtures of membrane curvature-stabilizing multivalent cationic lipids MVL3(3+) and MVL5(5+) with neutral 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC). In conjunction with prior work on MVLBG2(16+), our experiments suggest that BL and nanotube formation is a general phenomenon in membranes containing multivalent lipids, thus enhancing the relevance of BLs for applications such as gene/drug storage and delivery or templating.